Research workbench
Crystal structure of hera-lbd (Y537S) in complex with benzylbutylphtalate
Analyse Crystal structure of hera-lbd (Y537S) in complex with benzylbutylphtalate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MG6
- Type
- protein
- Length
- 489 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Nuclear receptor coactivator 1
- UniProt
- P03372, Q15788
- Ligands
- 27G
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 235 | 70% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 236 | 67% helix, 4% strand | P03372 |
| C, D | Nuclear receptor coactivator 1 | protein | 9 | 78% helix, 0% strand | Q15788 |
Ligands and binding sites
- 27G · benzyl butyl benzene-1,2-dicarboxylate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.85 | 0.97 | 24 | 27G |
| 2 | 300 | 0.81 | 0.91 | 32 | 27G |
| 3 | 70 | 0.60 | 0.89 | 16 | empty |
| 4 | 80 | 0.59 | 0.88 | 16 | empty |
| 5 | 287 | 0.58 | 0.77 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1754 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 528 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 517 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 4MG6 · Crystal structure of hERa-LBD (Y537S) in complex with benzylbutylphtalate · the same entry in another collection · chain A against A, TM-score 1.00
- P03372 · AlphaFold monomer V2.0 prediction for estrogen receptor (P03372) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P03372
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 4MG6 · PDBe 4MG6 · UniProt P03372 · UniProt Q15788
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